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maf_oncoplot.r突变注释文件分类可视化maftools
Rscript /share/nas1/zhangll/MAF/code/maf_oncoplot.r -h usage: /share/nas1/zhangll/MAF/code/maf_oncoplot.r [-h] -i maffile -m metadata -g group [-a additive [additive ...]] [-T topgene] [-l genelist [genelist ...]] [-t] [-o outdir] [-H height] [-W width] Mutation annotation file classification visualization:https://www.亿速云.com/article/1518 optional arguments: -h, --help show this help message and exit -i maffile, --maf maffile input the maf file[required] -m metadata, --meta metadata input metadata file path[required] -g group, --group group input group id in metadata file to classification visualization[required] -a additive [additive ...], --additive additive [additive ...] add additional class[optional,default: NULL] -T topgene, --top topgene Number of top genes displayed [optional, default: 20] -l genelist [genelist ...], --genelist genelist [genelist ...] the selected gene list to display [optional, default: NULL] -t, --showtitle whether show maftools title of plot [optional, default: False] -o outdir, --outdir outdir output file directory [default cwd] -H height, --height height the height of pic inches [default 8] -W width, --width width the width of pic inches [default 8]
-i 突变注释文件maf的路径,可从TCGA数据库中直接下载:
Hugo_Symbol |
Entrez_Gene_Id |
Center |
NCBI_Build |
Chromosome |
Start_Position |
End_Position |
Strand |
Variant_Classification |
MFN2 |
9927 |
WUGSC |
GRCh48 | |
chr1 |
12001777 |
12001777 | |
+ |
Missense_Mutation |
KCNG3 |
170850 |
WUGSC |
GRCh48 | |
chr2 |
42444578 |
42444578 | + | Missense_Mutation |
MAP2 |
4133 |
WUGSC | GRCh48 | |
chr2 |
209692762 | 209692762 | |
+ |
Missense_Mutation |
HEG1 |
57493 |
WUGSC |
GRCh48 | |
chr3 |
125010546 |
125010546 | |
+ |
Missense_Mutation |
PCDHB11 |
56125 |
WUGSC |
GRCh48 | |
chr5 |
141200541 |
141200541 | |
+ |
Missense_Mutation |
NSD1 |
64324 |
WUGSC |
GRCh48 | |
chr5 |
177294257 |
177294257 | |
+ |
Missense_Mutation |
F13A1 |
2162 |
WUGSC | GRCh48 | |
chr6 |
6174609 |
6174609 | |
+ |
Missense_Mutation |
PRRT4 |
401399 |
WUGSC |
GRCh48 | |
chr7 |
128359624 |
128359624 | |
+ |
Missense_Mutation |
FBP2 |
8789 |
WUGSC |
GRCh48 | |
chr9 |
94558941 |
94558941 | |
+ |
Missense_Mutation |
-m metadata文件,病人样本的各种特征信息,必须包含以patient命名的患者TCGA编号列:
patient |
sample |
shortLetterCode |
tumor_stage |
tissue_or_organ_of_origin | |
alcohol_history |
gender |
ethnicity |
race |
TCGA-M9-A5M8 |
TCGA-M9-A5M8-01A |
TP |
stage iia |
Lower third of esophagus |
Yes |
male |
not reported |
not reported |
TCGA-R6-A6DQ |
TCGA-R6-A6DQ-01B |
TP |
not reported |
Lower third of esophagus |
Yes |
female |
not hispanic or latino |
white |
TCGA-LN-A9FP |
TCGA-LN-A9FP-01A |
TP |
stage iia |
Middle third of esophagus | |
Yes |
female |
not hispanic or latino |
asian |
TCGA-LN-A4MQ |
TCGA-LN-A4MQ-01A |
TP |
stage iii |
Lower third of esophagus |
No |
male |
not hispanic or latino |
asian |
TCGA-JY-A93D |
TCGA-JY-A93D-01A |
TP |
stage iiic |
Lower third of esophagus |
Yes |
male |
not reported |
white |
TCGA-IG-A3YB |
TCGA-IG-A3YB-01A |
TP |
stage iiia |
Lower third of esophagus |
No |
male |
not hispanic or latino |
white |
TCGA-IC-A6RF |
TCGA-IC-A6RF-01A |
TP |
stage ia |
Middle third of esophagus |
Yes |
female |
not hispanic or latino |
white |
TCGA-VR-A8EX |
TCGA-VR-A8EX-01A |
TP |
stage iva |
Middle third of esophagus |
No |
male |
not reported |
not reported |
-g 指定metadata 分组列名,如果分组名字有空格,应该用引号引起来
-a 附加分组列名,结果将在图中显示
-T 可指定所要展示的top基因个数,默认20
-l 可指定所要展示的基因列表,基因之间用空格隔开,默认NULL
Rscript /share/nas1/zhangll/MAF/code/maf_oncoplot.r -i /share/nas1/zhangll/MAF/TCGA-ESCA.maf_maftools.maf -m /share/nas1/huangls/project/TCGA_ESCA/metadata.tsv -g gender
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